Huaijun Zhou, Ph.D.

Huaijun Zhou

Position Title
Professor and Chancellor’s Leadership Professor
Director of USAID Feed the Future Innovation Lab for Genomics to Improve Poultry

2247 Meyer Hall


  • M.S., Bioinformatics and Computational Biology, Iowa State University.
  • Ph.D., Immunogenetics and Molecular Genetics Iowa State University.

Honors and Awards

  • 2023 Chancellor's Leadership Professor
  • 2023 The National Academy of Sciences Prize in Food and Agriculture Sciences
  • 2020 Prize for Outstanding Achievement in Science, Agriculture and Agri-Food Canada
  • 2020 Chancellor’s Awards for International Engagement
  • 2018 Zoetis Fundamental Science Award (PSA)
  • 2016 - Evonik Degussa Award for Achievement in Poultry Science
  • 2014 - Chancellor’s Fellow
  • 2013 - The American Association of Immunologists Early Career Faculty Travel Award
  • 2011 - PSA Early Achievement Award for Research
  • 2010 - Hy-Line International Research Award
  • 2009 - Big 12 Faculty Fellowship
  • 2009 - Outstanding Overseas Young Investigator Award, NSF China
  • 2004 - Natural Sciences and Engineering Research Council of Canada (NSERC) Fellowship
  • 2002 - Research Excellence Award, Iowa State University   


Research Projects

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  • USDA NIFA project: Functional Annotation of Regulatory Elements in Livestock Species. This project is one of pilot projects of FAANG consortium (www. The overall goal of this project is to generate a comprehensive resource of functional genomic elements for the chicken, cattle, and pig genomes. Our specific goals are:  
  1. Annotate chromatin states corresponding to DNase hypersensitivity, four histone modifications, and one transcription factor
  2. Annotate promoters, enhancers, and silencers by integrating information from RNA-seq, DNAse-seq, and ChIP-seq against four histone modifications and one transcription factor.
  3. Freely distribute all raw and annotated data via UCSC Genome Browser and Ensembl.


  • NIH-NIFA Dual Purpose with Dual Benefits project: Development of Colonization Resistance in Chicks.
  • Our long-range goal is to understand the mechanisms that govern the interactions between the host and its gut-associated microbial communities. The objectives of this application are to study the mechanism of colonization resistance and devise strategies to prevent a bloom of Proteobacteria after hatching.
    • Specific Aim 1: Determine the mechanism by which obligate anaerobic bacteria confer colonization resistance against Proteobacteria in newly hatched chicks
    • Specific Aim 2: Determine whether a treatment that enhances colonization resistance accelerates development of a mature microbial community structure in newly hatched chicks.

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Graduate Groups

Courses Taught

  • Animal Health and Disease, offered in Spring (ANS 150)
  • Avian Biology, offered in Spring (AVS 100)


A full list of current and past lab members is available on the Zhou Laboratory website.

Selected Publications

Dr. Huaijun Zhou has published a total of 150 peer-reviewed papers, five book chapters and more than 240 peer-reviewed abstract and/or meeting proceedings.

Pan Z, Y. Wang, M. Wang, Y. Wang, X. Zhu, S. Gu, C. Zhong, L. An, M. Shan , J. Damas, M. M. Halstead, D. Guan, N. Trakooljul, K. Wimmers, Y. Bi, S. Wu, M. E. Delany, X. Bai, H.H. Cheng, C. Sun, N. Yang, X. Hu, H. A Lewin, L. Fang, H. Zhou. 2023. An atlas of regulatory elements in chicken: a resource for chicken genetics and genomics. Sci. Adv. 9,eade1204. DOI:10.1126/sciadv.ade1204

Sun, Y.H., Cui, H., Song, C. J. Shen, X. Zhuo, R. Wang, X.Yu, R. Ndamba, Q. Mu, H. Gu, D. Wang, G. G. Murthy, P. Li, F. Liang, L. Liu, Q. Tao, Y. Wang, S. Orlowski, Q. Xu, H. Zhou, J. Jagne, O. Gokcumen, N. Anthony, X. Zhao, and X. Li. Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity. Nat Commun 14, 812 (2023).

D. Guan, M. Halstead, A. D Islas-Trejo, D. Goszczynski, H. Cheng, P. J. Ross, H. Zhou. 2022. Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing. Front Genet. 2022 doi: 10.3389/fgene.2022.997460.

Y. Yao, S Liu,C. Xia, Y. Gao, Z. Pan, O. Canela‑Xandri, A. Khamseh, K. Rawlik, S. Wang, B. Li, Y. Zhang, E. Pairo‑Castineira, K. D’Mellow, X. Li, Z. Yan, C. Li, Y. Yu, S. Zhang, L. Ma, J. B. Cole, P. J. Ross, H. Zhou, C. Haley, G. E. Liu, L. Fang and A. Tenesa. 2022. Comparative transcriptome in large‑scale human and cattle populations. Genome Biology 23:176.

Pan, Z., Y. Yao, H. Yin, Z.Cai, Y. Wang, L. Bai, C. Kern, M. Halstead, G. Chanthavixay, N. Trakooljul, K. Wimmers, G. Sahana, G. Su, M. Lund, M. Fredholm, P. Karlskov-Mortensen, C. W. Ernst, P. Ross, C. K. Tuggle, L. Fang & H. Zhou. Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nat Commun 12, 5848 (2021).

KKZ Mon, C Kern, G Chanthavixay, Y Wang, H Zhou. 2021. Tolerogenic Immunoregulation towards Salmonella Enteritidis Contribute to Colonization Persistence in Young Chicks. Infect Immun doi: 10.1128/IAI.00736-20.

Aston EJ, Wang Y, Tracy KE, Gallardo RA, Lamont SJ. Zhou H. 2021. Comparison of cellular immune responses to avian influenza virus in two genetically distinct, highly inbred chicken lines. Vet Immunol Immunopathol. 235:110233. doi: 10.1016/j.vetimm.2021.110233.

M. Tixier-Boichard, S. FABRE, S. Dhorne-Pollet, A. Goubil, H. Acloque, S. Vincent-Naulleau, P. Ross, Y. Wang, G. Chanthavixay, H. Cheng, C. Ernst, V. Leesburg, E. Giuffra, H. Zhou. 2021. Tissue resources for the functional annotation of animal genomes" Frontiers in Genetics.

M. M. Halstead, D. E. Goszczynski, A. D. Islas-Trejo, H. Zhou and P. J. Ross. 2021. Large-scale multiplexing permits full-length transcriptome annotation of 32 bovine tissues from a single Nanopore flow cell. Front. Genet. | doi: 10.3389/fgene.2021.664260.

Kern, C., Wang, Y., Xu, X. M. Halstead, J. I. Korf, M. Delany, H. Cheng, J. F. Medrano, A. Van Eenennaam, C. W. Ernst. P. Flicek, G. Quon, J. Ross. Zhou, H. 2021. Functional genome annotations of three domestic animal species provide a vital resource for comparative and agricultural research. Nature Communications 12, 1821.

Daniel E. Goszczynski, Michelle M. Halstead, Alma D. Islas-Trejo, Huaijun Zhou and Pablo J. Ross 2021. Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage Genome Res. 31: 732-744

Kebschull JM, Richman EB, Ringach N, Friedmann D, Albarran E, Kolluru SS, Jones RC, Allen WE, Wang Y, Cho SW, Zhou H, Ding JB, Chang HY, Deisseroth K, Quake SR, Luo L. Cerebellar nuclei evolved by repeatedly duplicating a conserved cell-type set. Science. 2020 Dec 18;370(6523):eabd5059. doi: 10.1126/science.abd5059. PMID: 33335034.

Chanthavixay, K., C. Kern, Y. Wang, Saelao, P., R. Gallardo, S.J. Lamont, G. Rincon, Zhou, H. 2020. Integrated Transcriptome and Histone Modification Analysis Reveals NDV Infection Under Heat Stress Affects Bursa Development and Proliferation in Susceptible Chicken Line. Frontiers in Genetics.

Wang, Y, Saelao, K. Chanthavixay P., R. Gallardo, D,A, Bunn, S.J. Lamont. J.K. Dekkers, T. R. Kelly, Zhou, H. 2020. Liver Transcriptome Responses to Heat Stress and Newcastle Disease Virus Infection in Genetically Distinct Chicken Inbred Lines. Genes 11(9), 1067;

Ana Paula da Silva, E. Aston, G. Chiwanga, A. Birakos, A. Muhairwa, B. Kayang, T. Kelly, H. Zhou, RODRIGO GALLARDO 2020, Molecular Characterization of Newcastle Disease Viruses Isolated from Chickens in Tanzania and Ghana. Viruses  12, 916; doi:10.3390/v12090916

Walugembe M, Amuzu-Aweh EN, P. K. Botchway, A. Naazie, G. Aning, Wang Y, Saelao P, Kelly T, Gallardo RA, Zhou H, Lamont SJ, Kayang B.B., Dekkers JCM. 2020. Genetic Basis of Response of Ghanaian Local Chickens to Infection With a Lentogenic Newcastle Disease Virus. Front. Genet.,

Kim, T.H., C. Kern, and H. Zhou. 2020. Knockout of IRF7 Highlights its Modulator Function of Host Response Against Avian Influenza Virus and the Involvement of MAPK and TOR Signaling Pathways in Chicken. Genes 11, 385; doi:10.3390/genes11040385

K. K.Z. Mon, Y. Zhu, G. Chanthavixay, C. Kern and H. Zhou. 2020. Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken. Sci Rep. 10, Article number: 4809.

Halstead M., C. Kern, Saelao, P. G. Chanthavixay, Y. Wang, M. Delany, H. Zhou, P. Ross. 2020. Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues. Sci Rep 10, Article number: 5230.

Walugembe M, Mushi JR, Amuzu-Aweh EN, Chiwanga GH, Msoffe PL, Wang Y, Saelao P, Kelly T, Gallardo RA, Zhou H, Lamont SJ, Muhairwa AP, Dekkers JCM. 2019. Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus. Genes (Basel). 2019 Jul 17;10(7). pii: E546. doi: 10.3390/genes10070546.

Giuffra E, Tuggle CK; Archibald AL, Acloque H, Chamberlain AJ, Cochrane G, Daetwyler HD, Djebali S, Eory L, Foissac S, Goddard ME, Groenen MA, Halstead M, Harrison PW, Hayes BJ, Kern C, Khatib H, Kuo RI, MacHugh DE, Macleod IM, Madsen O, Reecy JM, Ross PJ, Watson M, Wells JM, Zhou H. 2019. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. Annu Rev Anim Biosci. 7:65-88. doi: 10.1146/annurev-animal-020518-114913.

Litvak Y., K.K.Z. Mon, H. Nguyen, G. Chanthavixay, M. Liou, E. M. Velazquez, L. Kutter, M. A. Alcantara, M. X. Byndloss, C.R. Tiffany, G. T. Walker, F. Faber, Y. Zhu, D. N. Bronner, A. J. Byndloss, R. M. Tsolis, H. Zhou. A. J. Baumler. 2019. Commensal Enterobacteriaceae protect against Salmonella colonization by competing for oxygen. Cell Host & Microbes 25, 1-12

Saelao, P., Y. Wang, G. Chanthavixay, V. Yu, J. Dekkers, R. Gallardo, T.R. Kelly, S.J. Lamont. Zhou, H. 2018. Integrated proteomic and transcriptomic analysis of differential expression of chicken lung tissue in response to NDV infection during heat stress. Genes 9, 579; doi:10.3390/genes9120579

Kim, T.H. and H. Zhou. 2018. Overexpression of chicken IRF7 increased viral replication and programmed cell death to the avian influenza virus infection through TGF-beta/FoxO signaling axis in DF-1. Frontiers in Genetics. doi: 10.3389/fgene.2018.00415.

Saelao, P., Y. Wang, K. Chanthavixay, J. Dekkers, R. Gallardo, T.R. Kelly, S.J. Lamont. H. Zhou. 2018. Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment. BMC Veterinary Research

Kern, C. P. P. Saelao, Y. Wang, M. Halstead, J. L. Chitwood, I. Korf, M. Delany, H. Cheng, J. F. Medrano, A. Van Eenennaam, C. W. Ernst. J. Ross, H. Zhou. 2018. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics

K. Rowland. Wolc. J. H. Zhou, R. Gallardo, T. Kelly, A. Dekkers, Lamont. S.J. 2018. Genome-wide association study of a commercial egg laying line challenged with Newcastle disease virus. Front. Genet., |

Wilson B. K, T. Kelly, D.A. Bunn, and H. Zhou. 2018. Key criteria and models for implementing a sustainable chicken breeding and distribution program for smallholder poultry producers. Livestock Research for Rural Development. 30 (4), Article #67. Retrieved April 13, 2018,

Zhang J, Kaiser MG, Deist MS, Gallardo RA, Bunn DA, Kelly TR, Dekkers JCM, Zhou H, Lamont SJ. Transcriptome Analysis in Spleen Reveals Differential Regulation of Response to Newcastle Disease Virus in Two Chicken Lines. Sci Rep. 2018 Jan 19;8(1):1278. doi: 10.1038/s41598-018-19754-8.

Zar Mon, K. K., P. Saelao, M. M. Halstead, G. Chanthavixay, H.-C. Chang, L. Garas, E. A Maga and H. Zhou. 2016. Salmonella enterica serovars Enteritidis infection alters the indigenous microbiota diversity in young layer chicks. Front. Vet. Sci. - Veterinary Infectious Diseases. 2:61. doi: 10.3389/fvets.2015.00061.

Li J, Li R, Wang Y, Hu X, Zhao Y, Li L, Feng C, Gu X, Liang F, Lamont S, Hu S, Zhou H*, Li N. 2015. Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq. BMC Genomics, 16 :851 (23 October 2015)

Kim, T.H, H. Zhou. 2015. Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown: 10.1371/journal.pone.0133450.

Schmid M. et al. H. Zhou. 2015.Third Report on Chicken Genes and Chromosomes.  Cytogenet Genome Res 145:78-179 (DOI:10.1159/000430927).

 Leif, A. et al. H. Zhou, The FAANG Consortium.  2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16:57. DOI: 10.1186/s13059-015-0622-4

Abernathy, J., Li, X., Jia, X., Chou, W., Lamont, S.J., Crooijmans, R., and Zhou, H. 2014. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization. Animal Genetics. doi: 10.1111/age.12141.

Wang Y, Lupiani B, Reddy S, S. J. Lamont, Zhou H. 2014. RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens. Poultry Science. 93(2):485-93. doi: 10.3382/ps.2013-03557.

Wang, Y., V. Brahmakshatriya, B. Lupiani, S. M Reddy, B. Soibam, A. L Benham, P. Gunaratne, H.Liu, M. Trakooljul, N. Ing, R. Okimoto and H. Zhou 2012. Integrated Analysis of microRNA Expression and mRNA Transcriptome in Lungs of Avian Influenza Virus Infected Broilers. BMC Genomics 13:278 (Highly assessed)

Wang Y, N. Ghaffari, C. D. Johnson, U. M. Braga-Neto, H. Wang, R. Chen, H. Zhou. 2011 Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. BMC Bioinformatics 12: doi:10.1186/1471-2105-12-S10-S5.

Li X., C. L. Swaggerty, M. H. Kogut, H. Chiang, Y. Wang, K. J. Genovese, H. He, H. Zhou. 2010. Gene expression profiling of the local cecal response of genetic chicken lines that differ in their susceptibility to Campylobacter jejuni colonization. PLoS ONE 5(7): e11827. doi:10.1371/journal.pone.0011827

Wang Y., V. Brahmakshatriya, B. Lupiani, S. Reddy, B. Yoon, H. Zhu, P. Gunaratne, R. Chen, J. Wang, H. Zhou. 2009. Identification of differentially expressed microRNAs In chicken lung and trachea with avian influenza virus infection by Solexa Sequencer. BMC Genomics 10:512. (Highly assessed)

Chiang, H.I., C. Swaggerty, M. Kogut, S. Dowd, X. Li, I. Pevzner, and H. Zhou. 2008. Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44K Agilent microarray. BMC Genomics 9:526.

Li, X.Y, H.I. Chiang, J. Zhu, S. Dowd and H. Zhou. 2008. Characterization of newly developed chicken 44K Agilent microarray. BMC Genomics 9:60. (Highly assessed)

Wong, G. K., H Zhou et al.  2004.  A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.  Nature 432:717-722.